Structure-wise discrimination of adenine and guanine by proteins on the basis of their nonbonded interactions

We have analyzed the nonbonded interactions of the structurally similar moieties, adenine and guanine forming complexes with proteins. The results comprise (a) the amino acid–ligand atom preferences, (b) solvent accessibility of ligand atoms before and after complex formation with proteins, and (c) preferred amino acid residue atoms involved in the interactions. We have observed that the amino acid preferences involved in the hydrogen bonding interactions vary for adenine and guanine. The structural variation between the purine atoms is clearly reflected by their burial tendency in the solvent environment. Correlation of the mean amino acid preference values show the variation that exists between adenine and guanine preferences of all the amino acid residues. All our observations provide evidence for the discriminating nature of the proteins in recognizing adenine and guanine.     

Self-association of glutamic acid-rich fusion peptide analogs of influenza hemagglutinin in the membrane-mimic environments: Effects of positional difference of glutamic acids on side chain ionization constant and intra- and inter-peptide interactions deduced from NMR and gel electrophoresis measurements

Two glutamic acid-rich fusion peptide analogs of influenza hemagglutinin were synthesized to study the organization of the charged peptides in the membranous media. Fluorescence and gel electrophoresis experiments suggested a loose association between the monomers in the vesicles. A model was built which showed that a positional difference of 3, 7 and 4, 8 results in the exposure of Glu3 and Glu7 side chains to the apolar lipidic core. Supportive results include: first, pK_a values of two pH units higher than reference value in aqueous medium for Glu3 and Glu7 CγH, whereas the deviation of pK_a from the reference value for Glu4 and Glu8 CγH is substantially smaller; second, Hill coefficients of titration shift of these protons indicate anti-cooperativity for Glu3 and Glu7 side chain protons but less so for Glu4 and Glu8, implying a strong electrostatic interaction between Glu3 and Glu7 possibly resulting from their localization in an apolar environment; third, positive and larger titration shift for NH of Glu3 is observed compared to that of Glu4, suggesting stronger hydrogen bond between the NH and the carboxylic group of Glu3 than that of Glu4, consistent with higher degree of exposure to hydrophobic medium for the side chain of Glu3.     

色氨酸残基在磷酸烯醇式丙酮酸羧化酶催化功能中的作用

在pH7.5条件下,用NBS对PEP羧化酶中色氨酸残基进行共价修饰表明,PEP羧化酶中48个色氨酸残基均能被NBS修饰。用邹承鲁图解法求得,其中4个残基为酶表现催化活性所必需的。 PEP羧化酶的变构效应剂G6P、Gly及Mal分别与酶预保温后,再经NBS修饰,前两种处理中,同样浓度的NBS所用修饰的色氨酸残基数和处理后的残存酶活与对照相比有很大的差异,而用Mal处理的,两者与对照相差无几。     

Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds.

The local environment of an amino acid in a folded protein determines the acceptability of mutations at that position. In order to characterize and quantify these structural constraints, we have made a comparative analysis of families of homologous proteins. Residues in each structure are classified according to amino acid type, secondary structure, accessibility of the side chain, and existence of hydrogen bonds from the side chains. Analysis of the pattern of observed substitutions as a function of local environment shows that there are distinct patterns, especially for buried polar residues. The substitution data tables are available on diskette with Protein Science. Given the fold of a protein, one is able to predict sequences compatible with the fold (profiles or templates) and potentially to discriminate between a correctly folded and misfolded protein. Conversely, analysis of residue variation across a family of aligned sequences in terms of substitution profiles can allow prediction of secondary structure or tertiary environment.     

长叶车前花叶病毒(HRV_(sh))外壳蛋白赖氨酸残基的修饰

我们曾报道长叶车前花叶病毒上海分离株(简称HRVsh)的外壳蛋白有二个赖氨酸残基,在PH8.5无变性剂存在的条件下,完整病毒颗粒表面的赖氨酸残基可与三硝基苯磺酸(TNPS)起反应,反应后的TNP-HRVsh病毒颗粒的感染力丧失达90％以上。 本文又进行了甲基乙亚胺甲酯(MEI)对HRVsh赖氨酸残基的修饰反应,修饰后的MEI-HRVsh病毒颗粒的感染力也同样丧失90％以上。 从三硝基苯磺酸修饰的病毒颗粒(TNP-HRVsh)中分离得到的RNA能与天然的HRVsh的外壳蛋白重建病毒颗粒,并具有感染力,说明修饰过程中核酸并不受影响。 进一步用同位素~(35)S,~(32)P双标记病毒,再以TNPS修饰标记的病毒,得到(~(35)S,~(32)P)-HRVsh及TNP-(~(35)S,~(32)P)-HRVsh。将两者分别接种于系统寄主青菜(Brassica chinensis)的一片叶片,一天后在非接种叶片上都可测得~(35)S,~(32)P的放射计数。其中,(~(35)S,~(32)P)-HRVsh的~(35)S/~(32)P比值降低了,而TNP-(~(35)S,~(32)P)-HRVsh的~(35)S/~(32)P比值保持不变。说明HRVsh外壳蛋白赖氨酸残基的修饰并不影响病毒颗粒进入寄主细胞,以及在寄主细胞间的转移。同位素双标记的结果表明,其感染力丧失的原因可能是由于上述修饰作用阻止了病毒在感染中所必须的脱壳过程。     

Physiological aspects of Taxus brevifolia seeds in relation to seed storage characteristics

Water relations, desiccation tolerance and longevity of Taxus brevifolia (Nutt.) seeds were studied to determine the optimal stage of development and storage conditions for seeds of this species. Seeds equilibrated to a range of relative humidities (RHs) had unusually low water contents which can be accounted for by the high lipid content of gametophyte tissues (71% of the dry mass). Water relations of embryonic tissue were more typical of those reported for other seed species. The water content below which freezing transitions were not observable in the embryo was ca 0.24 g H₂O (g dry weight)⁻¹ (g g⁻¹) for all maturity classes studied. Embryos did not achieve significant levels of desiccation tolerance (survival to water contents less than 0.5 g g⁻¹) until the latter stages of development when dry matter was maximal. Mature embryos could be dried to 0.025 g g⁻¹ (seed water content of 0.010 g g⁻¹) with no loss of viability. Thus, at the latter stages of development, embryo water content could be optimized to avoid both desiccation and freezing damage. Survival of mature seeds declined over a 2-year period when seeds were stored at temperatures between 5 and 35°C and RHs between 14 and 75%, corresponding to seed water contents between 0.015 and 0.07 g g⁻¹. The deterioration rate was slowest for seeds stored at the lowest RH and temperature. Our data indicate that seeds of Taxus brevifolia show orthodox rather than recalcitrant storage characteristics, but that the optimum water content for storage was extremely low. The results suggest that even if stored at optimal water contents and low temperatures, T. brevifolia seeds will be relatively short lived. The high quantity of lipids or reducing sugars may be contributing factors in the poor storage characteristics.     

Transmissibility of Bacterial Endosymbionts Between Isolates of Acanthamoeba Spp.

ABSTRACT. Experimental transmission of two bacterial endosymbionts to symbiont-free isolates of Acanthamoeba spp. was studied to determine specificity of the host-symbiont relationship. Both symbionts originated from amoebic isolates displaying an identical mitochondrial DNA Eco RI fingerprint (group AcUW II). Symbioses were readily established in one amoebic isolate which displayed a homologous mtDNA fingerprint (group AcUW II). Exposure of a heterologous amoebic isolate (group AcUW IV) to the two symbionts resulted in either cell death or encystation without the establishment of symbioses. While symbioses were established with an amoebic isolate from a second heterologous group (AcUW I), a unique membranous sheath appeared and persisted around one of the symbionts which did not exist in the original host. An isolate representing a third heterologous amoebic group (AcUW VI) was variable in its susceptibility with one symbiont unable to infect the host and the other becoming established only after an initial reaction in which trophozoites rounded-up and floated off the substrate. These studies suggest that a specific recognition system exists between particular isolates of Acanthamoeba and their symbionts, and that the appearance of a killer phenotype is related to contact between mismatched, though recognized, pairs.